Genomics Metabolics, Genoscope, François Jacob Institute, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057, Evry, France.
Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78352, Jouy-en-Josas, France.
Nat Commun. 2022 Aug 29;13(1):5082. doi: 10.1038/s41467-022-32661-x.
Here we introduce the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enables one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Standard formats like SBML and SBOL are used throughout to enforce the compatibility of the tools. In a study carried out at four different sites, we illustrate the link between pathway design and engineering with the building of a library of E. coli lycopene-producing strains. We also benchmark our workflows on literature and expert validated pathways. Overall, we find an 83% success rate in retrieving the validated pathways among the top 10 pathways generated by the workflows.
在这里，我们介绍 Galaxy-SynBioCAD 门户，这是一个合成生物学、代谢工程和工业生物技术的工具库。该门户上目前共享的工具和工作流程使人们能够构建产生所需化学目标的菌株库，涵盖从菌株和目标选择、要组装的 DNA 部件设计到驱动用于质粒组装和菌株转化的液体处理机的脚本生成的端到端代谢途径设计和工程过程。在整个过程中使用 SBML 和 SBOL 等标准格式来强制工具的兼容性。在四个不同地点进行的一项研究中，我们通过构建一个大肠杆菌番茄红素生产菌株库来说明途径设计和工程之间的联系。我们还根据文献和专家验证的途径对我们的工作流程进行了基准测试。总的来说，我们发现工作流程生成的前 10 条途径中，有 83%的途径能够成功检索到经过验证的途径。
